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MCL coexpression mm9:1740: Difference between revisions

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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0.180840494114715,0.107744855247029,0.0913378685245542,0,0.0642873521037868,0.180011747370744,0.31155146000515,0,0,0,0.212433811736393,0.226747351639347,0.153628809860867,0,0.0786677159214676,0,0.0644551523736777,0,0,0,0,0,0,0,0,0,0,0,0,0,0.638314809848069,0.2507456850819,0.311127917657318,0.441647142913664,0.484176860335644,0.534984022513845,0,0,0,0,0,0,0,0,0,0.524909504503017,0.236880264493592,0.125836948423969,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.100004302423367,0,0,0,0,0,0,0,0,0,0,0,0.0866592903778752,0,0,0,0,0,0.0491463288895459,0.204093579732844,0.0519509775191307,0,0,0,0,0,0,0,0,0.0509235292940968,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0994554632344034,0.108620321524749,0,0,0,0,0,0,0,0,0,0,0,0,0.0592603993571966,0,0,0,0,0,0.101901855392646,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0736278867910527,0,0,0,0,0,0,0,0,0,0,0,0.0691813633419548,0,0,0.188620766046218,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.179727725901961,0,0.0737896374598673,0,0.055643654597214,0.0894734883806707,0.0681778550615498,0.056886356216389,0.0562185712770556,0,0,0,0,0,0,0,0,0,0,0.209873913294111,0,0,0,0,0,0,0,0,0,0,0,0.411629065605499,0,0.0424616899933645,0.10031596050676,0.31684229110821,0.529452974228686,0.342808339754772,0.36720785254731,0.547055771425622,0.331042861818472,0.449458548076044,0.336358567251731,0.61053016743986,0.696689599292719,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=
|ontology_enrichment_celltype=CL:0000988!1.61e-14!32;CL:0002032!1.61e-14!32;CL:0000037!1.61e-14!32;CL:0000566!1.61e-14!32;CL:0000837!1.61e-14!32;CL:0000838!1.28e-12!12;CL:0000542!1.77e-11!13;CL:0000051!1.77e-11!13;CL:0000791!4.76e-11!9;CL:0000789!4.76e-11!9;CL:0002420!4.76e-11!9;CL:0002419!4.76e-11!9;CL:0000790!4.76e-11!9;CL:0000084!5.55e-11!11;CL:0000827!5.55e-11!11;CL:0002031!1.67e-10!25;CL:0000738!3.91e-10!17;CL:0002087!3.91e-10!17;CL:0000624!1.07e-09!8;CL:0002242!6.47e-09!16;CL:0002320!1.21e-08!46;CL:0000134!1.21e-08!46;CL:0000893!7.93e-07!6;CL:0002489!7.93e-07!6;CL:0000898!7.93e-07!6;CL:0000809!7.93e-07!6;CL:0000810!7.93e-07!6;CL:0000895!7.93e-07!6;CL:0000808!7.93e-07!6;CL:0000894!7.93e-07!6;CL:0000806!7.93e-07!6;CL:0000807!7.93e-07!6;CL:0000805!7.93e-07!6;CL:0002425!7.93e-07!6;CL:0002436!7.93e-07!6;CL:0002427!7.93e-07!6;CL:0002428!7.93e-07!6;CL:0002429!7.93e-07!6;CL:0002433!7.93e-07!6;CL:0002431!7.93e-07!6;CL:0002432!7.93e-07!6
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!3.55e-26!48;UBERON:0002405!3.55e-26!48;UBERON:0004177!5.32e-25!29;UBERON:0005057!5.32e-25!29;UBERON:0002390!1.62e-24!45;UBERON:0003061!1.62e-24!45;UBERON:0003408!1.10e-23!24;UBERON:0002370!3.40e-22!23;UBERON:0000974!3.40e-22!23;UBERON:0004807!3.40e-22!23;UBERON:0005058!3.40e-22!23;UBERON:0003351!3.40e-22!23;UBERON:0009113!3.40e-22!23;UBERON:0003295!3.40e-22!23;UBERON:0009722!3.40e-22!23;UBERON:0005562!3.40e-22!23;UBERON:0007690!3.40e-22!23;UBERON:0006562!4.69e-21!24;UBERON:0001557!4.69e-21!24;UBERON:0001042!4.69e-21!24;UBERON:0008814!4.69e-21!24;UBERON:0009145!4.69e-21!24;UBERON:0000077!1.20e-19!35;UBERON:0000072!3.79e-18!27;UBERON:0007811!5.29e-14!36;UBERON:0001004!5.97e-14!42;UBERON:0000063!7.36e-13!35;UBERON:0000065!7.40e-13!41;UBERON:0003081!1.03e-11!87;UBERON:0000153!6.92e-11!43;UBERON:0000926!9.69e-09!120;UBERON:0004120!9.69e-09!120;UBERON:0006603!9.69e-09!120;UBERON:0002384!1.21e-08!46;UBERON:0001041!1.32e-07!80;UBERON:0000490!3.25e-07!66
}}

Latest revision as of 17:25, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr1:135960097..135960108,+p@chr1:135960097..135960108
+
Mm9::chr1:138031733..138031746,-p@chr1:138031733..138031746
-
Mm9::chr4:63047044..63047062,+p@chr4:63047044..63047062
+
Mm9::chr7:121461031..121461042,-p@chr7:121461031..121461042
-
Mm9::chrX:45496807..45496816,-p@chrX:45496807..45496816
-


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

no results for this coexpression

Relative expression of the co-expression cluster over median <br>Analyst:




Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
hematopoietic cell1.61e-1432
hematopoietic oligopotent progenitor cell1.61e-1432
hematopoietic stem cell1.61e-1432
angioblastic mesenchymal cell1.61e-1432
hematopoietic multipotent progenitor cell1.61e-1432
lymphoid lineage restricted progenitor cell1.28e-1212
lymphocyte1.77e-1113
common lymphoid progenitor1.77e-1113
mature alpha-beta T cell4.76e-119
alpha-beta T cell4.76e-119
immature T cell4.76e-119
mature T cell4.76e-119
immature alpha-beta T cell4.76e-119
T cell5.55e-1111
pro-T cell5.55e-1111
hematopoietic lineage restricted progenitor cell1.67e-1025
leukocyte3.91e-1017
nongranular leukocyte3.91e-1017
CD4-positive, alpha-beta T cell1.07e-098
nucleate cell6.47e-0916
connective tissue cell1.21e-0846
mesenchymal cell1.21e-0846
thymocyte7.93e-076
double negative thymocyte7.93e-076
naive T cell7.93e-076
double-positive, alpha-beta thymocyte7.93e-076
CD4-positive, alpha-beta thymocyte7.93e-076
naive thymus-derived CD4-positive, alpha-beta T cell7.93e-076
DN4 thymocyte7.93e-076
DN1 thymic pro-T cell7.93e-076
DN2 thymocyte7.93e-076
DN3 thymocyte7.93e-076
immature single positive thymocyte7.93e-076
early T lineage precursor7.93e-076
mature CD4 single-positive thymocyte7.93e-076
resting double-positive thymocyte7.93e-076
double-positive blast7.93e-076
CD69-positive double-positive thymocyte7.93e-076
CD69-positive, CD4-positive single-positive thymocyte7.93e-076
CD4-positive, CD8-intermediate double-positive thymocyte7.93e-076
CD24-positive, CD4 single-positive thymocyte7.93e-076

Uber Anatomy
Ontology termp-valuen
hemolymphoid system3.55e-2648
immune system3.55e-2648
hemopoietic organ5.32e-2529
immune organ5.32e-2529
hematopoietic system1.62e-2445
blood island1.62e-2445
gland of gut1.10e-2324
thymus3.40e-2223
neck3.40e-2223
respiratory system epithelium3.40e-2223
hemolymphoid system gland3.40e-2223
pharyngeal epithelium3.40e-2223
thymic region3.40e-2223
pharyngeal gland3.40e-2223
entire pharyngeal arch endoderm3.40e-2223
thymus primordium3.40e-2223
early pharyngeal endoderm3.40e-2223
pharynx4.69e-2124
upper respiratory tract4.69e-2124
chordate pharynx4.69e-2124
pharyngeal arch system4.69e-2124
pharyngeal region of foregut4.69e-2124
mixed endoderm/mesoderm-derived structure1.20e-1935
segment of respiratory tract3.79e-1827
craniocervical region5.29e-1436
respiratory system5.97e-1442
organ segment7.36e-1335
respiratory tract7.40e-1341
lateral plate mesoderm1.03e-1187
anterior region of body6.92e-1143
mesoderm9.69e-09120
mesoderm-derived structure9.69e-09120
presumptive mesoderm9.69e-09120
connective tissue1.21e-0846
foregut1.32e-0780
unilaminar epithelium3.25e-0766


TFBS overrepresentation<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs




JASPAR motifs


Motifs-log10(p-value)
MA0003.10.211284
MA0004.10.603793
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.10.0502051
MA0017.11.14026
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.11.10192
MA0029.10.995171
MA0030.11.00195
MA0031.12.2151
MA0038.10.757669
MA0040.11.07552
MA0041.10.522007
MA0042.10.507715
MA0043.11.1618
MA0046.11.09955
MA0048.10.205696
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.602741
MA0056.10
MA0057.10.192781
MA0058.10.50032
MA0059.10.513699
MA0060.10.330907
MA0061.10.364227
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.10.573319
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.12.86731
MA0074.10.708108
MA0076.11.1853
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.148348
MA0089.10
MA0090.10.566938
MA0091.10.617887
MA0092.10.567278
MA0093.10.440484
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.10.248108
MA0106.10.809991
MA0107.10.454197
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.10.949408
MA0115.11.16466
MA0116.10.419688
MA0117.11.13165
MA0119.11.30068
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.10.869325
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.11.73051
MA0139.10.295945
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.10.476962
MA0146.10.822925
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.22.01551
MA0035.20.700704
MA0039.20.489701
MA0138.20.861035
MA0002.20.809945
MA0137.20.479301
MA0104.20.315156
MA0047.20.75686
MA0112.20.157681
MA0065.22.84751
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.203217
MA0155.10.515751
MA0156.11.18326
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.10.245828
MA0163.11.29282
MA0164.10.729558
MA0080.22.01158
MA0018.20.739807
MA0099.20.854449
MA0079.23.38617
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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